Bioinfo Services

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The bioinformatic facility aims to provide the research groups located within CEINGE, with a large selection of software tools, useful in the analysis of nucleic acid and protein sequence as well as other typical biological data, such as images.

The available tools include the full EMBOSS package, a vast collection of general purpose and more specific sequence handling programs, database search programs, such as FASTA and BLAST, CLUSTALW, programs from the PHYLIP package, a number of programs typically used for protein modelling and RNA structure analysis. Most programs are easily accessible through a Web interface, although command line access remains an option for researchers more familiar with the Unix interface. Fast and prompt execution of the programs is guaranteed by a 112 processor cluster, acting in concert with a number of smaller, multiprocessor servers; program execution is transparently uploaded to the cluster without any specific intervention from the user.

A web application developed within the group, CAPRI, allows access to the programs in a global, collective application which is run on the server, but from the point of view of the user it behaves as a typical desktop application, running on each client connected to the system.

About 100 public databases are stored in-house, and the data are kept updated by mirroring: every night updates are downloaded from their primary repositories and integrated with the already available data. Access to the databases is through the SRS interface, also installed and maintained locally by the bioinformatic group (http://srs.ceinge.unina.it); the SRS installation available at CEINGE is one of the most complete in the world in terms of number of databases available and linked tools. The whole ENSEMBL genome browser, complete with all fully sequenced genomes, is also mirrored locally and made available to the users (http://ensembl.ceinge.unina.it).

The described services, are currently offered to researchers located in other institutions in the area of Napoli, including DBBM, IGB, BIOGEM, DBPCM. Most services are also made available to the research community through our public web site http://bioinfo.ceinge.unina.it, although with some limitations due to data not publicly available and to the excessive load that a public server would pose for programs requiring higher processing power.

The available tools

The available tools include over 200 programs for DNA and protein sequence manipulation, molecular prediction, and statistical data analysis. In addition about 100 public databases are maintained and updated daily. The tools may be grouped as follows:



Bioinformatics: Bioinformatic services - Research Activity - IT Services - The Bioinformatics Group
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